jbrowse-plugin-mafviewer 1.5.0 → 1.5.1

package/dist/jbrowse-plugin-mafviewer.umd.production.min.js

@@ -6,7 +6,7 @@ ${W}`}).join(`
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extends Mp.FeatureRendererType{getExpandedRegion(t){let{start:o,end:r}=t,a=1;return{...t,start:Math.floor(Math.max(o-a,0)),end:Math.ceil(r+a)}}async render(t){let{regions:o,bpPerPx:r,samples:a,rowHeight:f,sessionId:n,adapterConfig:l,highResolutionScaling:u=1}=t,s=o[0],d=a.length*f+100,i=(s.end-s.start)/r,m=(0,ca.createCanvas)(Math.ceil(i*u),Math.ceil(d*u)),p=m.getContext("2d");if(!p)throw new Error("Could not get canvas context");u!==1&&p.scale(u,u);let{renderingContext:x,sampleToRowMap:h,region:g}=Fp(p,t),{dataAdapter:T}=await Bt(this.pluginManager,n,l),w=T,c=this.getExpandedRegion(s);await Pt(w.getFeatures(c,t),I=>{this.featurePassesFilters(t,I)&&Dp(I,g,r,h,x)});let{flatbush:A,items:C}=kp(x,a);return{imageData:await(0,ca.createImageBitmap)(m),flatbush:A,items:C,samples:a,features:new Map,width:i,height:d,containsNoTransferables:!0}}};var De=S(D()),Pp=S(Xe());var Lp=S(xe()),ng=(0,Lp.observer)(function(e){let{items:t,displayModel:o,height:r,samples:a,flatbush:f}=e,n=(0,De.useRef)(null),l=(0,De.useMemo)(()=>It.from(f),[f]),[u,s]=(0,De.useState)(!1),d=(0,De.useCallback)((i,m)=>{let p=0,x=0;if(n.current){let A=n.current.getBoundingClientRect();p=i-A.left,x=m-A.top}let h=l.search(p,x,p+1,x+1);if(h.length===0)return;let T=h.find(A=>t[A]?.isInsertion)??h[0],w=T!==void 0?t[T]:void 0;if(!w)return;let c=a[w.rowIndex];return{...w,sampleId:c?.id??"unknown",sampleLabel:c?.label||c?.id||"unknown"}},[l,t,a]);return De.default.createElement("div",{ref:n,onClick:i=>{let m=d(i.clientX,i.clientY);m?.isInsertion&&o.showInsertionSequenceDialog?.({sequence:m.base,sampleLabel:m.sampleLabel,chr:m.chr,pos:m.pos})},onMouseMove:i=>{let m=d(i.clientX,i.clientY);o.setHoveredInfo?.(m),o.setHighlightedRowNames?.(m?.sampleId?[m.sampleId]:void 0),s(!!m?.isInsertion)},onMouseLeave:()=>{o.setHoveredInfo?.(void 0),o.setHighlightedRowNames?.(void 0),s(!1)},style:{overflow:"visible",position:"relative",height:r,cursor:u?"pointer":"default"}},De.default.createElement(Pp.PrerenderedCanvas,{...e,style:{position:"absolute",left:0}}))}),Np=ng;var Hp=S(ze());var lg=(0,Hp.ConfigurationSchema)("LinearMafRenderer",{},{explicitlyTyped:!0}),Wp=lg;function vn(e){e.addRendererType(()=>new Jo({name:"LinearMafRenderer",ReactComponent:Np,configSchema:Wp,pluginManager:e}))}var Up=S(Je()),Vp=S(ve());var F=S(D()),ot=S(Xe()),fo=S(se()),_p=S(ve()),q=S($e()),Gp=S(st()),sg=(0,Gp.makeStyles)()(e=>({textbox:{width:"100%"},paper:{margin:e.spacing(),padding:e.spacing()},submit:{marginTop:25,marginBottom:100,display:"block"}}));function Qn({model:e}){let{classes:t}=sg(),[o,r]=(0,F.useState)(""),[a,f]=(0,F.useState)(),[n,l]=(0,F.useState)(),[u,s]=(0,F.useState)(),[d,i]=(0,F.useState)(),[m,p]=(0,F.useState)("MAF track"),[x,h]=(0,F.useState)("BigMafAdapter"),[g,T]=(0,F.useState)("TBI"),w=(0,_p.getRoot)(e);return F.default.createElement(q.Paper,{className:t.paper},F.default.createElement(q.Paper,null,d?F.default.createElement(ot.ErrorMessage,{error:d}):null,F.default.createElement(q.FormControl,null,F.default.createElement(q.FormLabel,null,"File type"),F.default.createElement(q.RadioGroup,{value:x,onChange:c=>{h(c.target.value)}},["BigMafAdapter","MafTabixAdapter","BgzipTaffyAdapter"].map(c=>F.default.createElement(q.FormControlLabel,{key:c,value:c,control:F.default.createElement(q.Radio,null),checked:x===c,label:c})))),x==="BigMafAdapter"?F.default.createElement(ot.FileSelector,{location:a,name:"Path to bigMaf",rootModel:w,setLocation:c=>{f(c)}}):x==="MafTabixAdapter"?F.default.createElement(F.default.Fragment,null,F.default.createElement(q.FormControl,null,F.default.createElement(q.FormLabel,null,"Index type"),F.default.createElement(q.RadioGroup,{value:x,onChange:c=>{T(c.target.value)}},["TBI","CSI"].map(c=>F.default.createElement(q.FormControlLabel,{key:c,value:c,control:F.default.createElement(q.Radio,null),checked:g===c,label:c})))),F.default.createElement(ot.FileSelector,{location:a,name:"Path to MAF tabix",rootModel:w,setLocation:c=>{f(c)}}),F.default.createElement(ot.FileSelector,{location:n,name:"Path to MAF tabix index",rootModel:w,setLocation:c=>{l(c)}})):F.default.createElement(F.default.Fragment,null,F.default.createElement(ot.FileSelector,{location:a,name:"Path to TAF.gz (Bgzipped TAF)",rootModel:w,setLocation:c=>{f(c)}}),F.default.createElement(ot.FileSelector,{location:n,name:"Path to TAF.gz.tai (TAF index)",rootModel:w,setLocation:c=>{l(c)}}))),F.default.createElement("div",null,F.default.createElement(ot.FileSelector,{location:u,name:"Path to newick tree (.nh)",rootModel:w,setLocation:c=>{s(c)}}),F.default.createElement(q.TextField,{multiline:!0,rows:10,value:o,onChange:c=>{r(c.target.value)},helperText:"Sample names (optional if .nh supplied, required if not)",placeholder:"Enter sample names from the MAF file, one per line, or JSON formatted array of samples",variant:"outlined",fullWidth:!0})),F.default.createElement(q.TextField,{value:m,helperText:"Track name",onChange:c=>{p(c.target.value)}}),F.default.createElement(q.Button,{variant:"contained",className:t.submit,onClick:()=>{try{let c=(0,fo.getSession)(e),A=[];try{A=JSON.parse(o)}catch{A=o.split(/\n|\r\n|\r/)}let C=[`${m.toLowerCase().replaceAll(" ","_")}-${Date.now()}`,c.adminMode?"":"-sessionTrack"].join("");(0,fo.isSessionWithAddTracks)(c)&&(c.addTrackConf({trackId:C,type:"MafTrack",name:m,assemblyNames:[e.assembly],adapter:x==="BigMafAdapter"?{type:x,bigBedLocation:a,samples:A,nhLocation:u}:x==="MafTabixAdapter"?{type:x,bedGzLocation:a,nhLocation:u,index:{indexType:g,location:n},samples:A}:{type:x,tafGzLocation:a,taiLocation:n,nhLocation:u,samples:A}}),e.view?.showTrack(C)),e.clearData(),(0,fo.isSessionModelWithWidgets)(c)&&c.hideWidget(e)}catch(c){i(c)}}},"Submit"))}function Fn(e){e.addAddTrackWorkflowType(()=>new Up.AddTrackWorkflowType({name:"MAF track",ReactComponent:Qn,stateModel:Vp.types.model({})}))}var Ko=class{name;maybeDisplayName;constructor(t){this.name=t?.name||"UNKNOWN",this.maybeDisplayName=t?.displayName}get displayName(){return this.maybeDisplayName||this.name}};var dg=Symbol("mapObjectSkip"),Kp=e=>typeof e=="object"&&e!==null,Jp=e=>{if(!Kp(e)||e instanceof RegExp||e instanceof Error||e instanceof Date||e instanceof Map||e instanceof Set||e instanceof WeakMap||e instanceof WeakSet||e instanceof Promise||e instanceof ArrayBuffer||e instanceof DataView||ArrayBuffer.isView(e)||globalThis.Blob&&e instanceof globalThis.Blob)return!1;let t=e;return!(typeof t.$$typeof=="symbol"||typeof t.asymmetricMatch=="function")},ug=(e,t)=>{if(t){let o=Object.keys(e),r=Object.getOwnPropertySymbols(e).filter(a=>Object.getOwnPropertyDescriptor(e,a)?.enumerable);return[...o,...r]}return Object.keys(e)},Dn=(e,t,o,r=new WeakMap)=>{let{target:a={},deep:f=!1,includeSymbols:n=!1}=o??{},l={deep:f,includeSymbols:n};if(r.has(e))return r.get(e);r.set(e,a);let u=s=>s.map(d=>Jp(d)?Dn(d,t,l,r):d);if(Array.isArray(e))return u(e);for(let s of ug(e,l.includeSymbols)){let d=e[s],i=t(s,d,e);if(i===dg)continue;if(!Array.isArray(i))throw new TypeError(`Mapper must return an array or mapObjectSkip, got ${i===null?"null":typeof i}`);if(i.length<2)throw new TypeError(`Mapper must return an array with at least 2 elements [key, value], got ${i.length} elements`);let[m,p,{shouldRecurse:x=!0}={}]=i;if(m!=="__proto__"){l.deep&&x&&Jp(p)&&(p=Array.isArray(p)?u(p):Dn(p,t,l,r));try{a[m]=p}catch(h){if(h instanceof TypeError&&h.message.includes("read only"))continue;throw h}}}return a};function kn(e,t,o){if(!Kp(e))throw new TypeError(`Expected an object, got \`${e}\` (${typeof e})`);if(Array.isArray(e))throw new TypeError("Expected an object, got an array");return Dn(e,(a,f)=>t(a,f,e),o)}function ig(e,t,o=new WeakSet){let r=f=>{let n=ip(f.handleId);if(!n)throw new Error(`File not in cache for handleId: ${f.handleId}. The file "${f.name}" may need to be reopened.`);let l=`fh-blob-${f.handleId}`;return t[l]=n,{locationType:"BlobLocation",name:f.name,blobId:l}},a=f=>{if(!(!f||typeof f!="object"||o.has(f)))if(o.add(f),Array.isArray(f))for(let n=0;n<f.length;n++){let l=f[n];ln(l)?f[n]=r(l):a(l)}else{let n=f;for(let l of Object.keys(n)){let u=n[l];ln(u)?n[l]=r(u):a(u)}}};a(e)}var Yo=class e extends Ko{pluginManager;constructor(t){super(),this.pluginManager=t}async serializeArguments(t,o){return await this.augmentLocationObjects(t,o),{...t,blobMap:wn()}}async serializeNewAuthArguments(t,o){let r=this.pluginManager.rootModel;if(!fn(r)||t.internetAccountPreAuthorization)return t;let a=r.findAppropriateInternetAccount(t);return a&&(t.internetAccountPreAuthorization=await a.getPreAuthorizationInformation(t)),t}async deserializeArguments(t,o){return t.blobMap&&up(t.blobMap),t}async executeDirect(t){}supportsDirectExecution(){return this.executeDirect!==e.prototype.executeDirect}async serializeReturn(t,o,r){return t}async deserializeReturn(t,o,r){let a;try{a=await t}catch(f){if(zi(f)){let n=this.pluginManager.rootModel?.createEphemeralInternetAccount(`HTTPBasicInternetAccount-${new URL(f.url).origin}`,{},f.url);throw new la("Retrying with created internet account",n.internetAccountId)}throw f}return Xi(a)?a.value:a}async augmentLocationObjects(t,o){let r=this.pluginManager.rootModel,a=[],f=wn(),{renderingProps:n,...l}=t;if(ig(l,f),kn(l,(u,s)=>{if(nn(s)&&a.push(s),Array.isArray(s))for(let d of s)nn(d)&&a.push(d);return[u,s]},{deep:!0}),fn(r)&&r.internetAccounts.length===0)return t;for(let u of a)await this.serializeNewAuthArguments(u,o);return t}};var qo=class e{filterChain;constructor({filters:t,jexl:o}){this.filterChain=t.map(r=>r.trim()).filter(r=>!!r).map(r=>{if(typeof r=="string")return{expr:ji(r,o),string:r};throw new Error(`invalid inputFilter string "${r}"`)})}passes(...t){for(let o of this.filterChain)if(!o.expr.eval({feature:t[0]}))return!1;return!0}toJSON(){return{filters:this.filterChain.map(t=>t.string)}}static fromJSON(t){return new e(t)}};var Et=class extends Yo{async deserializeArguments(t,o){return{...await super.deserializeArguments(t,o),filters:t.filters?new qo({filters:t.filters,jexl:this.pluginManager.jexl}):void 0}}async serializeArguments(t,o){let a=this.pluginManager.rootModel?.session?.assemblyManager;if(!a)throw new Error("no assembly manager");let f=await pp(a,{...t,filters:t.filters?.toJSON().filters});return super.serializeArguments(f,o)}};var jo=class extends Et{name="MafGetSamples";async execute(t,o){let r=this.pluginManager,a=await this.deserializeArguments(t,o),{regions:f,adapterConfig:n,sessionId:l}=a,{dataAdapter:u}=await Bt(r,l,n);return u.getSamples(f,a)}};function Mn(e){e.addRpcMethod(()=>new jo(e))}function Yp({regions:e,showAllLetters:t,samples:o,features:r,includeInsertions:a}){let f=e[0],n=new Map(o.map((d,i)=>[d.id,i])),l=f.end-f.start,u=o.map(()=>new Array(l).fill("-")),s=new Map;for(let d of r.values()){let i=d.get("start"),m=d.get("alignments"),p=d.get("seq");for(let[x,h]of Object.entries(m)){let g=h.seq,T=n.get(x);if(T===void 0)continue;let w=u[T];for(let c=0,A=0,C=g.length;c<C;c++){let I=p[c];if(I!=="-"){let R=g[c],B=i+A-f.start;if(B>=0&&B<l){if(R==="-")w[B]="-";else if(R!==" "){let E=R.toLowerCase();t?w[B]=E:I.toLowerCase()===E?w[B]=".":w[B]=E}}A++}else if(a){let R="";for(;c<g.length&&p[c]==="-";){let B=g[c];R+=B!=="-"&&B!==" "?B.toLowerCase():"-",c++}if(c--,R.length>0){let B=i+A-f.start;if(B>=0&&B<=l){let E=s.get(B)||[];E.push({sequence:R,sampleIndex:T}),s.set(B,E)}}}}}}return a&&s.size>0?pg(u,s,o.length):u.map(d=>d.join(""))}function pg(e,t,o){let r=[...t.keys()].sort((a,f)=>f-a);for(let a of r){let f=t.get(a),n=0;for(let u of f)u.sequence.length>n&&(n=u.sequence.length);let l=new Map;for(let u of f)l.set(u.sampleIndex,u.sequence);for(let u=0;u<o;u++){let s=e[u],d=l.get(u);if(d){let i=d.padEnd(n,"-");s.splice(a,0,...i.split(""))}else{let i=new Array(n).fill("-");s.splice(a,0,...i)}}}return e.map(a=>a.join(""))}var zo=class extends Et{name="MafGetSequences";async execute(t,o){let r=await this.deserializeArguments(t,o),{samples:a,regions:f,adapterConfig:n,sessionId:l,showAllLetters:u,includeInsertions:s}=r,d=(await Bt(this.pluginManager,l,n)).dataAdapter,i=await Tn(d.getFeatures(f[0],r).pipe(Sn()));return Yp({features:new Map(i.map(m=>[m.id(),m])),samples:a,regions:f,showAllLetters:u,includeInsertions:s})}};function Pn(e){e.addRpcMethod(()=>new zo(e))}var zm=S(D()),Xm=S(jp());var em=S(D());var Aa=S(D()),zp=S(se());var Xp=S(xe()),$p=S(st()),mg=(0,$p.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:Ji(e.palette.primary.main).alpha(.4).toRgbString(),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),xg=(0,Xp.observer)(function({model:t}){let{classes:o}=mg(),r=(0,zp.getSession)(t),{assemblyManager:a}=r,f="widgets"in r?r.widgets:void 0;if(!f)return null;let n=[];for(let[,l]of f){let u=l;if(u.type==="MafSequenceWidget"&&u.connectedViewId===t.id){let s=l,{hoverHighlight:d}=s;if(d){let{refName:i,start:m,end:p,assemblyName:x}=d,g=a.get(x)?.getCanonicalRefName(i)??i,T=t.bpToPx({refName:g,coord:m}),w=t.bpToPx({refName:g,coord:p});if(T&&w){let c=Math.min(T.offsetPx,w.offsetPx)-t.offsetPx,A=Math.max(Math.abs(w.offsetPx-T.offsetPx),3);n.push(Aa.default.createElement("div",{key:`maf-hover-${s.id}`,className:o.highlight,style:{left:c,width:A}}))}}}}return Aa.default.createElement(Aa.default.Fragment,null,n)}),Zp=xg;function Ln(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t,o)=>{let r=o.model;return[...t,em.default.createElement(Zp,{key:"maf-sequence-hover-highlight",model:r})]})}var tm=S(ze()),om=(0,tm.ConfigurationSchema)("MafSequenceWidget",{});var rt=S(ve());function rm(){return rt.types.model("MafSequenceWidget",{id:rt.types.identifier,type:rt.types.literal("MafSequenceWidget"),adapterConfig:rt.types.frozen(void 0),samples:rt.types.frozen(void 0),regions:rt.types.frozen(void 0),connectedViewId:rt.types.maybe(rt.types.string)}).volatile(()=>({hoverHighlight:void 0})).actions(e=>({setHoverHighlight(t){e.hoverHighlight=t}}))}function Xn(e){e.addWidgetType(()=>new Xm.default({name:"MafSequenceWidget",heading:"MAF Sequence",configSchema:om,stateModel:rm(),ReactComponent:(0,zm.lazy)(()=>Promise.resolve().then(()=>(jm(),qm)))})),Ln(e)}var ax=S(Je());var $m=S(pr()),Zm=S(se()),ex=S(mr()),tx=S(xr()),ox=S(ve());var $o=class extends $m.BaseFeatureDataAdapter{setupP;async setupPre(){if(!this.getSubAdapter)throw new Error("no getSubAdapter available");return{adapter:(await this.getSubAdapter({...(0,ox.getSnapshot)(this.config),type:"BedTabixAdapter"})).dataAdapter}}async setupPre2(){return this.setupP||(this.setupP=this.setupPre().catch(t=>{throw this.setupP=void 0,t})),this.setupP}async setup(t){let{statusCallback:o=()=>{}}=t||{};return(0,Zm.updateStatus)("Downloading index",o,()=>this.setupPre2())}async getRefNames(t){let{adapter:o}=await this.setup(t);return o.getRefNames()}async getHeader(t){let{adapter:o}=await this.setup(t);return o.getHeader()}getFeatures(t,o){return(0,tx.ObservableCreate)(async r=>{let{adapter:a}=await this.setup(o),f="",n=this.getConf("refAssemblyName");await Pt(a.getFeatures(t,o),l=>{let u=l.get("field5").split(","),s={};for(let d=0,i=u.length;d<i;d++){let p=u[d].split(":"),[x,h,g,T,w,c]=p;if(!x||!c)continue;let{assemblyName:A,chr:C}=ms(x);A&&(f||(f=A),s[A]={chr:C,start:+h,srcSize:+g,strand:T==="-"?-1:1,unknown:+w,seq:c})}r.next(new je(l.id(),l.get("start"),l.get("end"),l.get("refName"),0,s,xs(s,n,t.assemblyName,f)??""))}),r.complete()},o?.stopToken)}async getSamples(t){let o=this.getConf("nhLocation"),r=o.uri==="/path/to/my.nh"?void 0:await(0,ex.openLocation)(o).readFile("utf8");return{samples:lt(this.getConf("samples")),tree:r?Tt(r):void 0}}freeResources(){}};var $n=S(ze());var yg=(0,$n.ConfigurationSchema)("MafTabixAdapter",{samples:{type:"frozen",description:"string[] or {id:string,label:string,color?:string}[]",defaultValue:[]},bedGzLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi",locationType:"UriLocation"}},refAssemblyName:{type:"string",defaultValue:""},index:(0,$n.ConfigurationSchema)("Index",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi"}},indexType:{type:"string",defaultValue:"TBI"}}),nhLocation:{type:"fileLocation",description:"newick tree",defaultValue:{uri:"/path/to/my.nh",locationType:"UriLocation"}}},{explicitlyTyped:!0,preProcessSnapshot:e=>e.uri?{...e,...e.nhUri?{nhLocation:{uri:e.nhUri,baseUri:e.baseUri}}:{},bedGzLocation:{uri:e.uri,baseUri:e.baseUri},index:{location:{uri:`${e.uri}.tbi`,baseUri:e.baseUri}}}:e}),rx=yg;function Zn(e){return e.addAdapterType(()=>new ax.AdapterType({name:"MafTabixAdapter",AdapterClass:$o,configSchema:rx}))}var Sa=S(Je());var fx=S(ze()),nx=S(Je());function el(e){return(0,fx.ConfigurationSchema)("MafTrack",{},{baseConfiguration:(0,nx.createBaseTrackConfig)(e),explicitIdentifier:"trackId"})}function tl(e){return e.addTrackType(()=>{let t=el(e);return new Sa.TrackType({name:"MafTrack",configSchema:t,displayName:"MAF track",stateModel:(0,Sa.createBaseTrackModel)(e,"MafTrack",t)})})}var lx="1.5.1";var wa=class extends sx.default{name="MafViewerPlugin";version=lx;install(t){qa(t),ja(t),tl(t),Mf(t),vn(t),Zn(t),Fn(t),Pn(t),Mn(t),Xn(t)}configure(t){}};return Ax(Bg);})();
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 react-is/cjs/react-is.production.min.js: